Recombination of the porcine X chromosome: a high density linkage map

Fernández, Ana; Muñoz, María; Alves, E.; Folch, Josep María; Noguera, J. L.; Enciso, Miguel Pérez; Rodrı́guez, Marı́a del Carmen; Silió, L.

doi:10.1186/s12863-014-0148-x

Cited by 14 publications

(13 citation statements)

References 23 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…; Fernández et al . ), our data confirm that NPAR exhibits a much lower variability than that expected under neutrality, that is 3/4 of the autosomal diversity (θ A ). Here, θ NPAR ≤ 1/4 θ A or about one‐third of the expected diversity was observed, either in Asia or in Europe.…”

Section: Resultssupporting

confidence: 84%

The chimerical genome of Isla del Coco feral pigs (Costa Rica), an isolated population since 1793 but with remarkable levels of diversity

Bianco

Soto

Vargas³

et al. 2015

Molecular Ecology

View full text Add to dashboard Cite

The history of domestic species and of their wild ancestors is not a simple one, and feral processes can clarify key aspects of this history, including the adaptive processes triggered by new environments. Here, we provide a comprehensive genomic study of Isla del Coco (Costa Rica) feral pigs, a unique population that was allegedly founded by two individuals and has remained isolated since 1793. Using SNP arrays and genome sequencing, we show that Cocos pigs are hybrids between Asian and European pigs, as are modern international pig breeds. This conclusively shows that, as early as the 18th century, British vessels were loading crossbred pigs in Great Britain and transporting them overseas. We find that the Y chromosome has Asian origin, which has not been reported in any international pig breed. Chinese haplotypes seem to have been transmitted independently between Cocos and other pig breeds, suggesting independent introgression events and a complex pattern of admixing. Although data are compatible with a founder population of N = 2, variability levels are as high in Cocos pigs as in international pig breeds (~1.9 SNPs/kb) and higher than in European wild boars or local breeds (~1.7 SNPs/kb). Nevertheless, we also report a 10-Mb region with a marked decrease in variability across all samples that contains four genes (CPE, H3F3C, SC4MOL and KHL2) previously identified as highly differentiated between wild and domestic pigs. This work therefore illustrates how feral population genomic studies can help to resolve the history of domestic species and associated admixture events.

show abstract

Section: Resultssupporting

confidence: 84%

The chimerical genome of Isla del Coco feral pigs (Costa Rica), an isolated population since 1793 but with remarkable levels of diversity

Bianco

Soto

Vargas³

et al. 2015

Molecular Ecology

View full text Add to dashboard Cite

show abstract

“…; Fernández et al . , ,b) and genotype differences between tissues. The sequencing of cDNA from the same hypothalamic and hepatic samples confirmed that 25 out of the 32 detected SNPs were actual SNPs, representing 80% of the total number of tested SNPs.…”

Section: Resultsmentioning

confidence: 99%

“…Differential gene expression conditional on SNP genotypes that showed significant associations with production traits were evaluated here using the RNA‐Seq expression data (Fernández et al . ,b; Pérez‐Montarelo et al . ).…”

Section: Methodsmentioning

confidence: 99%

Using RNA‐Seq SNP data to reveal potential causal mutations related to pig production traits and RNA editing

et al. 2016

View full text Add to dashboard Cite

RNA-Seq technology is widely used in quantitative gene expression studies and identification of non-annotated transcripts. However this technology also can be used for polymorphism detection and RNA editing in transcribed regions in an efficient and cost-effective way. This study used SNP data from an RNA-Seq assay to identify genes and mutations underlying production trait variations in an experimental pig population. The hypothalamic and hepatic transcriptomes of nine extreme animals for growth and fatness from an (Iberian × Landrace) × Landrace backcross were analyzed by RNA-Seq methodology, and SNP calling was conducted. More than 125 000 single nucleotide variants (SNVs) were identified in each tissue, and 78% were considered to be potential SNPs, those SNVs segregating in the context of this study. Potential informative SNPs were detected by considering those showing a homozygous or heterozygous genotype in one extreme group and the alternative genotype in the other group. In this way, 4396 and 1862 informative SNPs were detected in hypothalamus and liver respectively. Out of the 32 SNPs selected for validation, 25 (80%) were confirmed as actual SNPs. Association analyses for growth, fatness and premium cut yields with 19 selected SNPs were carried out, and four potential causal genes (RETSAT, COPA, RNMT and PALMD) were identified. Interestingly, new RNA editing modifications were detected and validated for the NR3C1:g.102797 (ss1985401074) and ACSM2B:g.13374 (ss1985401075) positions and for the COG3:g3.4525 (ss1985401087) modification previously identified across vertebrates, which could lead to phenotypic variation and should be further investigated.

show abstract

“…The contribution of the X-chromosome to phenotypic variation might be important for fertility or reproduction traits, e.g. [ 10 – 12 ]. Examples include variants that affect litter size in sheep, e.g.…”

Section: Introductionmentioning

confidence: 99%

Theoretical and empirical comparisons of expected and realized relationships for the X-chromosome

Druet

Legarra

2020

Genet Sel Evol

View full text Add to dashboard Cite

Background: X-chromosomal loci present different inheritance patterns compared to autosomal loci and must be modeled accordingly. Sexual chromosomes are not systematically considered in whole-genome relationship matrices although rules based on genealogical or marker information have been derived. Loci on the X-chromosome could have a significant contribution to the additive genetic variance, in particular for some traits such as those related to reproduction. Thus, accounting for the X-chromosome relationship matrix might be informative to better understand the architecture of complex traits (e.g., by estimating the variance associated to this chromosome) and to improve their genomic prediction. For such applications, previous studies have shown the benefits of combining information from genotyped and ungenotyped individuals. Results: In this paper, we start by presenting rules to compute a genomic relationship matrix (GRM) for the X-chromosome (G X) without making any assumption on dosage compensation, and based on coding of gene content with 0/1 for males and 0/1/2 for females. This coding adjusts naturally to previously derived pedigree-based relationships (S) for the X-chromosome. When needed, we propose to accommodate and estimate dosage compensation and genetic heterogeneity across sexes via multiple trait models. Using a Holstein dairy cattle dataset, including males and females, we then empirically illustrate that realized relationships (G X) matches expectations (S). However, G X presents high deviations from S. G X has also a lower dimensionality compared to the autosomal GRM. In particular, individuals are frequently identical along the entire chromosome. Finally, we confirm that the heritability of gene content for markers on the X-chromosome that are estimated by using S is 1, further demonstrating that S and G X can be combined. For the pseudo-autosomal region, we demonstrate that the expected relationships vary according to position because of the sex-gradient. We end by presenting the rules to construct the 'H matrix' by combining both relationship matrices. Conclusions: This work shows theoretically and empirically that a pedigree-based relationship matrix built with rules specifically developed for the X-chromosome (S) matches the realized GRM for the X-chromosome. Therefore, applications that combine expected relationships and genotypes for markers on the X-chromosome should use S and G X .

show abstract

Recombination of the porcine X chromosome: a high density linkage map

Cited by 14 publications

References 23 publications

The chimerical genome of Isla del Coco feral pigs (Costa Rica), an isolated population since 1793 but with remarkable levels of diversity

The chimerical genome of Isla del Coco feral pigs (Costa Rica), an isolated population since 1793 but with remarkable levels of diversity

Using RNA‐Seq SNP data to reveal potential causal mutations related to pig production traits and RNA editing

Theoretical and empirical comparisons of expected and realized relationships for the X-chromosome

Contact Info

Product

Resources

About